From 3b96fac8bdda242f793d2930cf0c42977b9934d0 Mon Sep 17 00:00:00 2001
From: Philip Eisenlohr <eisenlohr@egr.msu.edu>
Date: Tue, 28 Nov 2017 10:59:53 -0500
Subject: [PATCH] added script to calculate numerical derivative of ASCIItable
 data

---
 processing/post/addDerivative.py | 121 +++++++++++++++++++++++++++++++
 1 file changed, 121 insertions(+)
 create mode 100755 processing/post/addDerivative.py

diff --git a/processing/post/addDerivative.py b/processing/post/addDerivative.py
new file mode 100755
index 000000000..85b5d2363
--- /dev/null
+++ b/processing/post/addDerivative.py
@@ -0,0 +1,121 @@
+#!/usr/bin/env python2.7
+# -*- coding: UTF-8 no BOM -*-
+
+import os,sys,math
+import numpy as np
+from optparse import OptionParser
+import damask
+
+scriptName = os.path.splitext(os.path.basename(__file__))[0]
+scriptID   = ' '.join([scriptName,damask.version])
+
+def derivative(coordinates,what):
+  
+  result = np.empty_like(what)
+  
+  # use differentiation by interpolation
+  # as described in http://www2.math.umd.edu/~dlevy/classes/amsc466/lecture-notes/differentiation-chap.pdf
+
+  result[1:-1,:] = + what[1:-1,:] * (2.*coordinates[1:-1]-coordinates[:-2]-coordinates[2:]) / \
+                     ((coordinates[1:-1]-coordinates[:-2])*(coordinates[1:-1]-coordinates[2:])) \
+                   + what[2:,:] * (coordinates[1:-1]-coordinates[:-2]) / \
+                     ((coordinates[2:]-coordinates[1:-1])*(coordinates[2:]-coordinates[:-2])) \
+                   + what[:-2,:] * (coordinates[1:-1]-coordinates[2:]) / \
+                     ((coordinates[:-2]-coordinates[1:-1])*(coordinates[:-2]-coordinates[2:])) \
+
+  result[0,:]    = (what[0,:] - what[1,:]) / \
+                   (coordinates[0] - coordinates[1])
+  result[-1,:]   = (what[-1,:] - what[-2,:]) / \
+                   (coordinates[-1] - coordinates[-2])
+
+  return result
+  
+# --------------------------------------------------------------------
+#                                MAIN
+# --------------------------------------------------------------------
+
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+Add column(s) containing numerical derivative of requested column(s) with respect to given coordinates.
+
+""", version = scriptID)
+
+parser.add_option('-c','--coordinates',
+                  dest = 'coordinates',
+                  type = 'string', metavar='string',
+                  help = 'heading of coordinate column')
+parser.add_option('-l','--label',
+                  dest = 'label',
+                  action = 'extend', metavar = '<string LIST>',
+                  help = 'heading of column(s) to differentiate')
+
+
+(options,filenames) = parser.parse_args()
+
+if options.coordinates is None:
+  parser.error('no coordinate column specified.')
+if options.label is None:
+  parser.error('no data column specified.')
+
+# --- loop over input files -------------------------------------------------------------------------
+
+if filenames == []: filenames = [None]
+
+for name in filenames:
+  try:    table = damask.ASCIItable(name = name,
+                                    buffered = False)
+  except: continue
+  damask.util.report(scriptName,name)
+
+# ------------------------------------------ read header ------------------------------------------
+
+  table.head_read()
+
+# ------------------------------------------ sanity checks ----------------------------------------
+
+  errors  = []
+  remarks = []
+  columns = []
+  dims    = []
+  
+  if table.label_dimension(options.coordinates) != 1:
+    errors.append('coordinate column {} is not scalar.'.format(options.coordinates))
+
+  for what in options.label:
+    dim = table.label_dimension(what)
+    if dim < 0: remarks.append('column {} not found...'.format(what))
+    else:
+      dims.append(dim)
+      columns.append(table.label_index(what))
+      table.labels_append('d({})/d({})'.format(what,options.coordinates) if dim == 1 else
+                         ['{}_d({})/d({})'.format(i+1,what,options.coordinates) for i in range(dim)]  )  # extend ASCII heade      table.labels_append('norm{}({})'.format(options.norm.capitalize(),what))                    # extend ASCII header with new labels
+
+  if remarks != []: damask.util.croak(remarks)
+  if errors  != []:
+    damask.util.croak(errors)
+    table.close(dismiss = True)
+    continue
+
+# ------------------------------------------ assemble header --------------------------------------
+
+  table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
+  table.head_write()
+
+# ------------------------------------------ process data ------------------------------------------
+
+  table.data_readArray()
+
+  mask = []
+  for col,dim in zip(columns,dims): mask += range(col,col+dim)                                      # isolate data columns to differentiate
+  
+  differentiated = derivative(table.data[:,table.label_index(options.coordinates)].reshape((len(table.data),1)),
+                              table.data[:,mask])                                                   # calculate numerical derivative
+  
+  table.data = np.hstack((table.data,differentiated))
+
+# ------------------------------------------ output result -----------------------------------------
+
+  table.data_writeArray()
+
+# ------------------------------------------ output finalization -----------------------------------  
+
+  table.close()                                                                                     # close ASCII tables